A total of 61 zooplankton taxa were found in the southwestern Caspian Sea between 1996 and 2010. Thirteen of them were meroplankton taxa and forty-eight were holoplankton taxa. The occurrence of 14 freshwater taxa indicated the influence of the Anzali wetland and river inflows. The decrease in zooplankton taxa was detected since 1996-1997 and continued till 2010. Pleopis polyphemoides, the only one out of the nine recorded Cladocera species in 1996-1997, was found after 2001. Similarly, of the five Copepoda species recorded in 1996-1997, only one, Acartia tonsa, was found abundant during the 2001–2010 sampling period. It was striking that many species which were abundant in the Caspian Sea in 1996-1997 were not found after 2000. Many reasons could have contributed to the changes in the zooplankton composition of the southern Caspian Sea, notably the serious environmental degradation since the early 1990s. It is also possible that invasive species might play a role in wiping out some sensitive endemic species.